LabAdviser/314/Microscopy 314-307/Postprocessing/Lattice fringes - Revision history

Jenk at 09:50, 8 September 2025

2025-09-08T09:50:09Z

← Older revision		Revision as of 11:50, 8 September 2025
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	(''content by Jakob Birkedal Wagner @DTU Nanolab, March 2020'')		(''content by Jakob Birkedal Wagner @DTU Nanolab, March 2020'')
	[[Category:314]]		[[index.php?title=Category:314]]
	[[Category:314-Microscopy]]		[[index.php?title=Category:314-Microscopy]]

	= Analysis of lattice fringe images (HRTEM) using Digital Micrograph =		= Analysis of lattice fringe images (HRTEM) using Digital Micrograph =

Jenk at 12:30, 27 March 2023

2023-03-27T12:30:12Z

← Older revision		Revision as of 14:30, 27 March 2023
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	'''Feedback to this page''': '''[mailto:labadviser@nanolab.dtu.dk?Subject=Feed%20back%20from%20page%20http://labadviser.nanolab.dtu.dk/index.php/LabAdviser/314/Microscopy_314-307/Postprocessing/Lattice_fringes click here]'''		'''Feedback to this page''': '''[mailto:labadviser@nanolab.dtu.dk?Subject=Feed%20back%20from%20page%20http://labadviser.nanolab.dtu.dk/index.php/LabAdviser/314/Microscopy_314-307/Postprocessing/Lattice_fringes click here]'''

	(''content by Jakob Birkedal Wagner, March 2020'')		(''content by Jakob Birkedal Wagner @DTU Nanolab, March 2020'')
	[[Category:314]]		[[Category:314]]
	[[Category:314-Microscopy]]		[[Category:314-Microscopy]]

Jenk: /* Lattice spacing in reciprocal space */

2022-09-20T08:22:35Z

Lattice spacing in reciprocal space

← Older revision		Revision as of 10:22, 20 September 2022
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	At times, it is easier to measure lattice space distances using Fast Fourier Transforms (FFTs). With the image of interest as active press Ctrl F in order to get an FFT of the image (see below):		At times, it is easier to measure lattice space distances using Fast Fourier Transforms (FFTs). With the image of interest as active press Ctrl F in order to get an FFT of the image (see below):

	[[File:Lattice-fringes_reciprocal_1.png\|600px\|thumb\|left\|Fig. 3:FFT of HRTEM image.]]		[[File:Lattice-fringes_reciprocal_1.png\|600px\|thumb\|left\|Fig. 3:FFT of HRTEM image.]]<br clear="all" />

	The complex FFT is by default shown as the logarithm of the modulus. The FFT is calibrated so it is possible to measure the lattice space distances directly by measuring the distance between the dominant Fourier components.		The complex FFT is by default shown as the logarithm of the modulus. The FFT is calibrated so it is possible to measure the lattice space distances directly by measuring the distance between the dominant Fourier components.

Jenk: /* Lattice spacing in reciprocal space */

2020-06-12T05:57:36Z

Lattice spacing in reciprocal space

← Older revision		Revision as of 07:57, 12 June 2020
Line 33:		Line 33:
	At times, it is easier to measure lattice space distances using Fast Fourier Transforms (FFTs). With the image of interest as active press Ctrl F in order to get an FFT of the image (see below):		At times, it is easier to measure lattice space distances using Fast Fourier Transforms (FFTs). With the image of interest as active press Ctrl F in order to get an FFT of the image (see below):

	[[File:Lattice-fringes_reciprocal_1.png\|600px\|thumb\|~~center~~\|Fig. 3:FFT of HRTEM image.]]		[[File:Lattice-fringes_reciprocal_1.png\|600px\|thumb\|left\|Fig. 3:FFT of HRTEM image.]]

	The complex FFT is by default shown as the logarithm of the modulus. The FFT is calibrated so it is possible to measure the lattice space distances directly by measuring the distance between the dominant Fourier components.		The complex FFT is by default shown as the logarithm of the modulus. The FFT is calibrated so it is possible to measure the lattice space distances directly by measuring the distance between the dominant Fourier components.

	[[File:Lattice-fringes_reciprocal_2.png\|500px\|thumb\|~~center~~\|Fig. 4:Measure in FFT.]]<br clear="all" />		[[File:Lattice-fringes_reciprocal_2.png\|500px\|thumb\|left\|Fig. 4:Measure in FFT.]]<br clear="all" />

	Here the distance between the Fourier components representing the same lattice space distance as analyzed above measured. The distance is d=5.59 nm-1, which can be coverted by taking the reciprocal value: d=2/d=2/5.59nm-1=3.58Å (here 2 reciprocal lattice space distances are measured, hence the ‘2’ in the calculation. The slight difference is due to the precision in the measurements and that the FFT here measures an average value over the image, while the direct space methods in this case is more local.		Here the distance between the Fourier components representing the same lattice space distance as analyzed above measured. The distance is d=5.59 nm-1, which can be coverted by taking the reciprocal value: d=2/d=2/5.59nm-1=3.58Å (here 2 reciprocal lattice space distances are measured, hence the ‘2’ in the calculation. The slight difference is due to the precision in the measurements and that the FFT here measures an average value over the image, while the direct space methods in this case is more local.
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	In order to get FFTs from smaller parts of the acquired micrograph, you have to define a region of interest (ROI) before you calculate the FFT:		In order to get FFTs from smaller parts of the acquired micrograph, you have to define a region of interest (ROI) before you calculate the FFT:

	[[File:Lattice-fringes_reciprocal_3.png\|600px\|thumb\|~~center~~\|Fig. 5:ROI tool.]]<br clear="all" />		[[File:Lattice-fringes_reciprocal_3.png\|600px\|thumb\|left\|Fig. 5:ROI tool.]]<br clear="all" />

	‘Right click’ on your image and choose the ‘Rectangle ROI’ tool (a). Mark the region of interest while holding down the ‘shift’ key. This way the ROI is restricted to a square making the FFT analysis more intuitive. After you have marked the ROI choose ‘Live FFT’ from the drop down menu (b). Now the outline of the ROI should become red.		‘Right click’ on your image and choose the ‘Rectangle ROI’ tool (a). Mark the region of interest while holding down the ‘shift’ key. This way the ROI is restricted to a square making the FFT analysis more intuitive. After you have marked the ROI choose ‘Live FFT’ from the drop down menu (b). Now the outline of the ROI should become red.
	Now it is possible to move the ROI around the micrograph while following the FFT ‘live’:		Now it is possible to move the ROI around the micrograph while following the FFT ‘live’:

	[[File:Lattice-fringes_reciprocal_4.png\|600px\|thumb\|~~center~~\|Fig. 6:ROI and live FFT (amorphous).]]<br clear="all" />		[[File:Lattice-fringes_reciprocal_4.png\|600px\|thumb\|left\|Fig. 6:ROI and live FFT (amorphous).]]<br clear="all" />

	[[File:Lattice-fringes_reciprocal_5.png\|600px\|thumb\|~~center~~\|Fig. 7:ROI and live FFT (crystaline).]]<br clear="all" />		[[File:Lattice-fringes_reciprocal_5.png\|600px\|thumb\|left\|Fig. 7:ROI and live FFT (crystaline).]]<br clear="all" />

Jenk: /* Lattice spacing in real space */

2020-06-12T05:57:14Z

Lattice spacing in real space

← Older revision		Revision as of 07:57, 12 June 2020
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	== Lattice spacing in real space ==		== Lattice spacing in real space ==

	[[File:Lattice-fringes_real_1.png\|600px\|thumb\|~~center~~\|Fig. 1:Lattice fringe image of InAs/InP with profile.]]<br clear="all" />		[[File:Lattice-fringes_real_1.png\|600px\|thumb\|left\|Fig. 1:Lattice fringe image of InAs/InP with profile.]]<br clear="all" />

	This image show a nice lattice fringe image of a InAs/InP nanowire. The distance of the lattice fringes running perpendicular to the nanowire direction can be measured by ‘right clicking’ on the image and choose the ‘profile’ icon (the ‘wavy’ icon below ‘A’ in the image. The you draw a line in the image and an intensity profile turns up. You can measure the distance of interest in the profile view. In this example 10 lattice space distances are measured to increase the measurement precision (d=3.54nm/10 = 3.54Å). If your image is a bit noisy the intensity profile can be averaged by ‘double clicking’ on the drawn profile in the image and enter the integration width (in pixels). An example of that is shown below:		This image show a nice lattice fringe image of a InAs/InP nanowire. The distance of the lattice fringes running perpendicular to the nanowire direction can be measured by ‘right clicking’ on the image and choose the ‘profile’ icon (the ‘wavy’ icon below ‘A’ in the image. The you draw a line in the image and an intensity profile turns up. You can measure the distance of interest in the profile view. In this example 10 lattice space distances are measured to increase the measurement precision (d=3.54nm/10 = 3.54Å). If your image is a bit noisy the intensity profile can be averaged by ‘double clicking’ on the drawn profile in the image and enter the integration width (in pixels). An example of that is shown below:

	[[File:Lattice-fringes_real_2.png\|500px\|thumb\|~~center~~\|Fig. 2:Profile measure.]]<br clear="all" />		[[File:Lattice-fringes_real_2.png\|500px\|thumb\|left\|Fig. 2:Profile measure.]]<br clear="all" />

	== Lattice spacing in reciprocal space ==		== Lattice spacing in reciprocal space ==

Jenk at 07:34, 28 May 2020

2020-05-28T07:34:37Z

← Older revision		Revision as of 09:34, 28 May 2020
Line 1:		Line 1:
	'''Feedback to this page''': '''[mailto:labadviser@nanolab.dtu.dk?Subject=Feed%20back%20from%20page%20http://labadviser.nanolab.dtu.dk/index.php/LabAdviser/314/Postprocessing/Lattice_fringes click here]'''		'''Feedback to this page''': '''[mailto:labadviser@nanolab.dtu.dk?Subject=Feed%20back%20from%20page%20http://labadviser.nanolab.dtu.dk/index.php/LabAdviser/314/Microscopy_314-307/Postprocessing/Lattice_fringes click here]'''

	(''content by Jakob Birkedal Wagner, March 2020'')		(''content by Jakob Birkedal Wagner, March 2020'')

Jenk: Jenk moved page LabAdviser/314/Postprocessing/Lattice fringes to LabAdviser/314/Microscopy 314-307/Postprocessing/Lattice fringes

2020-05-28T06:48:35Z

Jenk moved page LabAdviser/314/Postprocessing/Lattice fringes to LabAdviser/314/Microscopy 314-307/Postprocessing/Lattice fringes

← Older revision	Revision as of 08:48, 28 May 2020
(No difference)

Jenk at 14:34, 1 April 2020

2020-04-01T14:34:59Z

@@ Line 1: / Line 1: @@
 [[Category:314]]
 [[Category:314-Microscopy]]
@@ Line 48: / Line 51: @@
 [[File:Lattice-fringes_reciprocal_5.png|600px|thumb|center|Fig. 7:ROI and live FFT (crystaline).]]<br clear="all" />

Jenk at 09:10, 27 March 2020

2020-03-27T09:10:27Z

← Older revision		Revision as of 11:10, 27 March 2020
Line 1:		Line 1:
			[[Category:314]]
			[[Category:314-Microscopy]]

	= Analysis of lattice fringe images (HRTEM) using Digital Micrograph =		= Analysis of lattice fringe images (HRTEM) using Digital Micrograph =

Jenk at 12:38, 26 March 2020

2020-03-26T12:38:10Z

← Older revision		Revision as of 14:38, 26 March 2020
Line 17:		Line 17:
	== Lattice spacing in real space ==		== Lattice spacing in real space ==

	[[File:Lattice-fringes_real_1.png\|600px\|thumb\|center\|Fig. 1:Lattice fringe image of InAs/InP with profile.]]		[[File:Lattice-fringes_real_1.png\|600px\|thumb\|center\|Fig. 1:Lattice fringe image of InAs/InP with profile.]]<br clear="all" />

	This image show a nice lattice fringe image of a InAs/InP nanowire. The distance of the lattice fringes running perpendicular to the nanowire direction can be measured by ‘right clicking’ on the image and choose the ‘profile’ icon (the ‘wavy’ icon below ‘A’ in the image. The you draw a line in the image and an intensity profile turns up. You can measure the distance of interest in the profile view. In this example 10 lattice space distances are measured to increase the measurement precision (d=3.54nm/10 = 3.54Å). If your image is a bit noisy the intensity profile can be averaged by ‘double clicking’ on the drawn profile in the image and enter the integration width (in pixels). An example of that is shown below:		This image show a nice lattice fringe image of a InAs/InP nanowire. The distance of the lattice fringes running perpendicular to the nanowire direction can be measured by ‘right clicking’ on the image and choose the ‘profile’ icon (the ‘wavy’ icon below ‘A’ in the image. The you draw a line in the image and an intensity profile turns up. You can measure the distance of interest in the profile view. In this example 10 lattice space distances are measured to increase the measurement precision (d=3.54nm/10 = 3.54Å). If your image is a bit noisy the intensity profile can be averaged by ‘double clicking’ on the drawn profile in the image and enter the integration width (in pixels). An example of that is shown below:

	[[File:Lattice-fringes_real_2.png\|500px\|thumb\|center\|Fig. 2:Profile measure.]]		[[File:Lattice-fringes_real_2.png\|500px\|thumb\|center\|Fig. 2:Profile measure.]]<br clear="all" />

	== Lattice spacing in reciprocal space ==		== Lattice spacing in reciprocal space ==
Line 31:		Line 31:
	The complex FFT is by default shown as the logarithm of the modulus. The FFT is calibrated so it is possible to measure the lattice space distances directly by measuring the distance between the dominant Fourier components.		The complex FFT is by default shown as the logarithm of the modulus. The FFT is calibrated so it is possible to measure the lattice space distances directly by measuring the distance between the dominant Fourier components.

	[[File:Lattice-fringes_reciprocal_2.png\|500px\|thumb\|center\|Fig. 4:Measure in FFT.]]		[[File:Lattice-fringes_reciprocal_2.png\|500px\|thumb\|center\|Fig. 4:Measure in FFT.]]<br clear="all" />

	Here the distance between the Fourier components representing the same lattice space distance as analyzed above measured. The distance is d=5.59 nm-1, which can be coverted by taking the reciprocal value: d=2/d=2/5.59nm-1=3.58Å (here 2 reciprocal lattice space distances are measured, hence the ‘2’ in the calculation. The slight difference is due to the precision in the measurements and that the FFT here measures an average value over the image, while the direct space methods in this case is more local.		Here the distance between the Fourier components representing the same lattice space distance as analyzed above measured. The distance is d=5.59 nm-1, which can be coverted by taking the reciprocal value: d=2/d=2/5.59nm-1=3.58Å (here 2 reciprocal lattice space distances are measured, hence the ‘2’ in the calculation. The slight difference is due to the precision in the measurements and that the FFT here measures an average value over the image, while the direct space methods in this case is more local.
Line 37:		Line 37:
	In order to get FFTs from smaller parts of the acquired micrograph, you have to define a region of interest (ROI) before you calculate the FFT:		In order to get FFTs from smaller parts of the acquired micrograph, you have to define a region of interest (ROI) before you calculate the FFT:

	[[File:Lattice-fringes_reciprocal_3.png\|600px\|thumb\|center\|Fig. 5:ROI tool.]]		[[File:Lattice-fringes_reciprocal_3.png\|600px\|thumb\|center\|Fig. 5:ROI tool.]]<br clear="all" />

	‘Right click’ on your image and choose the ‘Rectangle ROI’ tool (a). Mark the region of interest while holding down the ‘shift’ key. This way the ROI is restricted to a square making the FFT analysis more intuitive. After you have marked the ROI choose ‘Live FFT’ from the drop down menu (b). Now the outline of the ROI should become red.		‘Right click’ on your image and choose the ‘Rectangle ROI’ tool (a). Mark the region of interest while holding down the ‘shift’ key. This way the ROI is restricted to a square making the FFT analysis more intuitive. After you have marked the ROI choose ‘Live FFT’ from the drop down menu (b). Now the outline of the ROI should become red.
	Now it is possible to move the ROI around the micrograph while following the FFT ‘live’:		Now it is possible to move the ROI around the micrograph while following the FFT ‘live’:

	[[File:Lattice-fringes_reciprocal_4.png\|600px\|thumb\|center\|Fig. 6:ROI and live FFT (amorphous).]]		[[File:Lattice-fringes_reciprocal_4.png\|600px\|thumb\|center\|Fig. 6:ROI and live FFT (amorphous).]]<br clear="all" />

	[[File:Lattice-fringes_reciprocal_5.png\|600px\|thumb\|center\|Fig. 7:ROI and live FFT (crystaline).]]		[[File:Lattice-fringes_reciprocal_5.png\|600px\|thumb\|center\|Fig. 7:ROI and live FFT (crystaline).]]<br clear="all" />